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CSB 2005 International IEEE Computer Society Computational Systems Bioinformatics Conference

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CSB
2005
IEEE

233views Bioinformatics» more CSB 2005»

PSIST: Indexing Protein Structures Using Suffix Trees

13 years 6 months ago

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Feng Gao, Mohammed Javeed Zaki

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Id	Views	Title	Status

1	233	PSIST: Indexing Protein Structures Using Suffix Trees	claim
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11	180	Functional Modularity in a Large-Scale Mammalian Molecular Interaction Network	claim
12	170	Cluster Utility: A New Metric for Clustering Biological Sequences	claim
13	168	cis-Regulatory Element Prediction in Mammalian Genomes	claim
14	167	Considerations in Making Microarray Cross-Platform Correlations	claim
15	167	SinicView: An Interactive Visualization Tool for Comparison of Multiple Sequence Alignment Results	claim
16	166	Artificial Neural Networks to Predict Daylily Hybrids	claim
17	166	Automated Validation of Polymerase Chain Reactions Using Amplicon Melting Curves	claim
18	165	Sequential Diagonal Linear Discriminant Analysis (SeqDLDA) for Microarray Classification and Gene Identification	claim
19	163	A symbolic approach to the simulation of biochemical models: application to circadian rhythms	claim
20	161	Data Integration in the Mouse Genome Informatics (MGI) Database	claim
21	160	Predicting Continuous Epitopes in Proteins	claim
22	156	A Robust Meta-classification Strategy for Cancer Diagnosis from Gene Expression Data	claim
23	155	Identifying Orthologs: Cycle Splitting on the Breakpoint Graph	claim
24	155	BioNavigation: Using Ontologies to Express Meaningful Navigational Queries Over Biological Resources	claim
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26	151	Analysis of SNP-Expression Association Matrices	claim
27	151	Lossless Compression of DNA Microarray Images	claim
28	149	Combinatorial method of splice sites prediction	claim
29	149	Similarity and cluster analysis algorithms for Microarrays using R trees	claim
30	147	Accurate Prediction of Orthologous Gene Groups in Microbes	claim
31	146	BioImage Data Mining and Informatics	claim
32	146	Multi-Metric and Multi-Substructure Biclustering Analysis for Gene Expression Data	claim
33	145	Data Mining in situ Gene Expression Patterns at Cellular Resolution	claim
34	145	Classification Methods for HIV-1 Medicated Neuronal Damage	claim
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37	142	BioMap: Discovering Schema Mapping Using Ontologies	claim
38	141	Joint Genomic and Metabolomic Analysis of Toxic Dose-Response Experiments	claim
39	141	Reconstructing Phylogenetic Networks Using Maximum Parsimony	claim
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41	140	HIV Structural and Biothermodynamics Databases: a Resource for the Pharmaceutical and Biotechnology Industry	claim
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44	139	Predicting gene function by combining expression and interaction data	claim
45	139	Open Microscopy Environment	claim
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48	139	Controlling Complexity	claim
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50	137	Improving Operon Prediction in E. coli	claim
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52	136	Computational Method for Temporal Pattern Discovery in Biomedical Genomic Databases	claim
53	136	Key Features of the UCSC Genome Site	claim
54	136	An Algebraic Geometry Approach to Protein Structure Determination from NMR Data	claim
55	136	Whole Genome Phylogeny Based on Clustered Signature String Composition	claim
56	135	Relating transcription factors, modules of genes and cultivation conditions in Saccharomyces cerevisiae	claim
57	135	Inverse Design of Large Molecules using Linear Diophantine Equations	claim
58	134	Predicting a Transcription Start Site: Case Study with Different Genomes	claim
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60	133	Choosing SNPs Using Feature Selection	claim
61	133	Investigation into Biomedical Literature Classification Using Support Vector Machines	claim
62	133	Biological Pathway Prediction from Multiple Data Sources Using Iterative Bayesian Updating	claim
63	133	Sequential Classification for Microarray and Clinical Data	claim
64	132	A Fast Shotgun Assembly Heuristic	claim
65	131	Phylogenetic Postprocessing	claim
66	131	Current Challenges in Bioimage Database Design	claim
67	130	iSimBioSys: An "In Silico" Discrete Event Simulation Framework for Modeling Biological Systems	claim
68	130	Integration of RNA Search methods for Identifying Novel Riboswitch Patterns in Eukaryotes	claim
69	130	TreeRefiner: A Tool for Refining a Multiple Alignment on a Phylogenetic Tree	claim
70	129	Reducing Gene Regulatory Networks by Decomposition	claim
71	129	Consensus Methods Using Phylogenetic Databases	claim
72	129	Rule Clustering and Super-rule Generation for Transmembrane Segments Prediction	claim
73	129	Minimal Marker Sets to Discriminate Among Seedlines	claim
74	129	Deformable Modeling for Improved Calculation of Molecular Velocities from Single-Particle Tracking	claim
75	129	A Pivoting Algorithm for Metabolic Networks in the Presence of Thermodynamic Constraints	claim
76	129	ssahaSNP A Polymorphism Detection Tool on a Whole Genome Scale	claim
77	128	Application of a Generalized MWC Model for the Mathematical Simulation of Metabolic Pathways Regulated by Allosteric Enzymes	claim
78	126	Visualization of Logic Analysis of Phylogenetic Profiles (LAPP)	claim
79	126	Discover True Association Rates in Multi-protein Complex Proteomics Data Sets	claim
80	126	Identifying Simple Discriminatory Gene Vectors with an Information Theory Approach	claim
81	126	A Tree-Decomposition Approach to Protein Structure Prediction	claim
82	125	Peptide Charge State Determination for Low-Resolution Tandem Mass Spectra	claim
83	125	Pathway Logic Helping Biologists Understand and Organize Pathway Information	claim
84	125	Discriminative Discovery of Transcription Factor Binding Sites from Location Data	claim
85	125	On Optimizing Distance-Based Similarity Search for Biological Databases	claim
86	125	Islands of Tractability for Parsimony Haplotyping	claim
87	124	Automated Characterization of cellular migration phenomena	claim
88	124	Multi-Scale Hierarchical Structure Prediction of Helical Transmembrane Proteins	claim
89	124	Identifying Local Gene Expression Patterns in Biomolecular Networks	claim
90	124	Discovering Functional Transcription Factor Binding from Superimposed Gene Networks	claim
91	121	K-means+ Method for Improving Gene Selection for Classification of Microarray Data	claim
92	121	Clustering Genes Using Gene Expression and Text Literature Data	claim
93	120	Chemical Structure-Activity Relationship Visualization Using Structure Activity Maps	claim
94	119	Temperature and Mutation Switches in the Secondary Structure of Small RNAs	claim
95	118	Gene Teams with Relaxed Proximity Constraint	claim
96	118	A Protein Interaction Verification System Based on a Neural Network Algorithm	claim
97	117	Protein Structure Prediction Using Physical-Based Global Optimization and Knowledge-Guided Fragment Packing	claim
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100	115	Incorporating life sciences applications in the architectural optimizations of next-generation petaflop-system	claim
101	115	A New Clustering Strategy with Stochastic Merging and Removing Based on Kernel Functions	claim
102	115	Mining Protein Sequence Motifs Representing Common 3D Structures	claim
103	114	Tree Decomposition Based Fast Search of RNA Structures Including Pseudoknots in Genomes	claim
104	114	EigenPhenotypes: Towards an Algorithmic Framework for Phenotype Discovery	claim
105	112	Robust and Accurate Cancer Classification with Gene Expression Profiling	claim
106	112	A Novel Quartet-Based Method for Phylogenetic Inference	claim
107	110	Maximum Sequence Alignment Fails to Predict Off-targeted Gene Regulation by RNAi	claim
108	110	A Topological Measurement for Weighted Protein Interaction Network	claim
109	109	Patterns of Gene Deletion following Genome Duplication in Yeast	claim
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111	98	Predicting functional gene-links from phylogenetic-statistical analyses of whole genomes	claim
112	98	Two-way clustering of gene expression profiles by sparse matrix factorization	claim

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